Chris Comer is out of a job. She was a nine-year veteran in the position of director of science curriculum for the Texas Education Agency (Texas-speak for the state’s “department of education”). The TEA administration essentially forced her resignation.

So, why would TEA do that? Comer forwarded an email from the National Center for Science Education announcing a talk by Dr. Barbara Forrest to several people with the following addition: “FYI”.

The call to fire Comer came from Lizzette Reynolds, who previously worked in the U.S. Department of Education. She also served as deputy legislative director for Gov. George W. Bush. She joined the Texas Education Agency as the senior adviser on statewide initiatives in January.

Reynolds, who was out sick the day Comer forwarded the e-mail, received a copy from an unnamed source and forwarded it to Comer’s bosses less than two hours after Comer sent it.

“This is highly inappropriate,” Reynolds said in an e-mail to Comer’s supervisors. “I believe this is an offense that calls for termination or, at the very least, reassignment of responsibilities.

How did that play out?

In documents obtained Wednesday through the Texas Public Information Act, agency officials said they recommended firing Comer for repeated acts of misconduct and insubordination. But Comer said she thinks political concerns about the teaching of creationism in schools were behind what she describes as a forced resignation.

Apparently, not being a team player in the The Republican War on Science is a firing offense at the TEA. Why forwarding an announcement concerning a talk whose topic is highly relevant to the conduct of science education by an internationally recognized speaker should cause TEA administrators a problem escapes me. One is forced to wonder whether Ms. Comer would be looking for a new job if instead she were forwarding emails announcing talks by DI fellows about “intelligent design” creationism.

(Read more (including the text of the offending email) at the Austringer and PZ Myer’s “Fear of Barbara Forrest” at Pharyngula)

I don’t think this has been blogged yet. Earlier this month BBC Radio 4 broadcast a double interview with Michael Majerus, oft-mentioned on PT for his peppered moth research, and Jerry Coyne, a well known evolutionary biologist and regular critic of ID/creationism, and an oft-cited critic of aspects of the peppered moth research.

Quentin Cooper, the reporter, does an excellent job reviewing the whole history of the situation, the influence of Coyne’s critique, and Majerus’s new results. The piece tells the key points of the whole complex story in just a few minutes. And at the end, Coyne basically says that it’s time for the peppered moths to go back into the textbooks, which is a significant thing to say given Coyne’s past criticisms.

In Rocks of Ages Stephen Jay Gould famously argued for Non-Overlapping Magisteria (NOMA), the notion that science and religion appropriately address different domains of knowledge (magisteria), and that therefore there is no necessary conflict between them so long as each sticks to its own domain. While that argument has its detractors, it was alive and well a few weeks ago in Ohio.

On November 14, with four high school science teachers I attended a panel presentation at the Center for Science and Industry in Columbus, the presentation being co-sponsored by COSI, the Ohio State University, and WOSU, the Columbus PBS station. The presentation was titled “The Intersection of Faith & Evolution: A Civil Dialogue.” The panelists were Jeff McKee, a paleontologist from Ohio State University, Patricia Princehouse, who lectures on evolutionary biology and philosophy at Case Western Reserve, David Ruppe, a pastor and scholar of religion, and Francis Collins, the Director of the Human Genome Project and an evangelical Christian. (I mention Collins’ religious affiliation because he was the only presenter for whom it was explicitly mentioned in the introductions.)

The event was heavily over-subscribed, with the organizers having to open several satellite venues with video feeds of the live event at COSI. Having got my reservation in early, I was in the second row in front of the panel along with one of the teachers, where we had easy access to the microphone for audience questions.

The show started with a short skit that had three teen-aged kids in sleeping bags talking about the age of the stars (billions vs. thousands of years), why they’re different (physics vs. begats), and whether one of the girls could be both a pastor and a scientist. The resolution, of course, was the claim that the two aren’t antithetical. (That it was a girl who felt that quandary was a tip-off to the general theological stance of the evening.)

The recent NOVA special about the Dover trial has given me a sense of deja vu, as the Discovery Institute predictably rehashes all of the bad arguments they made against the decision after it came out. As I’ve said in speeches about the trial, it took Judge Jones about 10 seconds to go from a conservative good old boy who wouldn’t dare sell out his benefactors (Bush and Santorum) to a self-aggrandizing liberal judicial activist out to destroy America.

In his latest screed on the DI blog, Casey Luskin puts his usual intellectual dishonesty on display, falsely declaring that Judge Jones “admits” that his ruling was “activist” on the flimsy basis that he made a statement that Luskin is able to twist to fit his own anachronistic definition of judicial activism. Here is the rather absurd definition of judicial activism that he offers:

One of the joys of procrastination is that sometimes if you wait long enough, someone else really will take care of things. I mention that because Ed Brayton just did a good job dismantling Casey Luskin’s latest whine about how big bad Judge Jones was such a nasty judicial activist for daring to issue a ruling in the Dover, PA Intelligent Design case that addressed the question of whether or not ID is good science. I was planning a long and detailed post on the same thing, but now all that I have to do is highlight one point that Ed didn’t make in his post.

As Ed points out, there were a number of reasons for Jones to rule on that point. For starters, he had to look at that if he wanted to handle the case in front of him the same way that the Supreme Court handled its last creationism case. (That’s called following precedent.) He also needed to look at that point in order to apply the test commonly used by the Federal Courts when they look at Establishment Clause cases. (That’s also called following precedent.) As Ed also notes, both the plaintiffs and the defendants specifically asked the judge to rule on that point.

What Ed doesn’t mention is that the plaintiffs and the defendants were not the only ones who asked Judge Jones to rule on whether or not Intelligent Design is good science:

I enjoyed celebrating Thanksgiving by being thankful for the people in my life. I just hope that such e-mailers were able to let go of their intense anger and hatred and find some reason for giving thanks over this holiday season.

On the other hand, we’ve got the official website for the upcoming Ben Stein movie “Expelled - No Intelligence Allowed” plugging a little video they’ve made called Darwin Daze Sock Hop.

Second-year dental student Emily Mackie said the university’s decision to call its inaugural Dundee Christmas Lecture “Why Evolution is Right … and Creationism is Wrong” is badly timed and insensitive to Christians.

The lecture is being given by Steve Jones, professor of genetics at University College, London, who claims that all biologists support the theory of evolution and that “intelligent design”—the belief that life was created as part of a divine plan—is wrong.

A blog devoted to shilling for Intelligent Design has posted a link to the paper by myself and Michael Weisberg critiquing attempts to apply evolutionary psychology to law. It appears the author of the post, one Denyse O’Leary, a Canadian journalist who is a notorious apologist for ID creationism, thought our article was of a piece with the skepticism about natural selection that is her raison d’etre. The second commenter appears to have noticed what Ms. O’Leary missed.

Ms O’Leary is also still in denial about processes of regularity and chance being able to generate information. While she has been insisting that her background does not allow her to evaluate the claims of ID when they involve science or mathematics, she surely seems to be accepting them as the Gospel.

Hint: Processes of variation and selection can trivially increase information in the genome. Even Dembski seems to have come to accept this and now he claims that such processes smuggle in information. Of course they do, they transfer information from the environment to the genome.

It doesn’t require a federal judge to figure out if ID/Creationism is a science or not.

Anyone can go through the list of activities of the ID/Creationists and pseudo-scientists and compare them to the activities of working scientists.

Do typical working scientists engage in the following activities when advancing new ideas?

Do they pitch them to naive audiences while complaining they can’t get a fair hearing in the science community? Do they form institutes that spend millions of dollars to crank out propaganda pushing their idea and criticizing the scientific community? Do they issue talking points to grass-roots organizations and political groups to be argued in churches and local newspapers around the country? Do they publish books on their ideas in the popular press and claim they are peer-reviewed?

Luskin argues that, based on an statements made by Judge Jones on the “Lehrer Newshour”, the ruling by Jones should be considered flawed:

Luskin Wrote:

First, Judge Jones admitted that a key question his ruling answered was whether intelligent design was “good science,” and he states that “after six weeks of largely expert testimony, I came to the conclusion that it simply was not good science” (emphasis added). This proves his judicial activism because it shows that, in his mind, a key question was not the constitutionality of Dover’s policy in particular, but rather a broad sweeping question about whether ID is “good science,” something that is totally inappropriate and unnecessary for the federal judiciary to answer in such a case over the constitutionality of a science curriculum.

Why is this claim so ironic? Well, if you read the submissions of the Discovery Institute to the judge, they argue that since ID is science, it cannot be ruled to be unconstitutional. In other words, they insist that the judge resolves the issue of ID being science. When he actually does this and he rules contrary to their expectations, the judge suddenly becomes an activist judge.

The Discovery Institute’s own website demonstrates that their amicus brief was submitted to argue “… about secular purposes for teaching about the scientific theory of intelligent design”” (October 31, 2005)

So what was the argument of the Discovery Institute which forced the judge to rule on the issue of ID being science?

There is a wonderful article in todays issue of Nature on bioluminescent organisms in the deep seas. We like to think of the deep seas as dark, since virtually no light filters into the abyssal depths from above. However, the deep sea abounds with bioluminescence, bacteria and sea life of all sorts glow gently in the depths, enough to seriously hamper the Antares deep sea neutrino telescope that is searching for the flashes of light the represent the rare interactions of neutrinos with other matter (subscription required).

As fascinating as bioluminescence is in its own right, the article links to an amazing paper. One that puts yet another dent (if that is possible) in Dr. Behe’s key thesis; that multi-amino acid binding sites are difficult to evolve. But how does the ability of a fish to see red refute a central argument of Dr. Behe’s “Edge of Evolution”

A recent discovery in stem cell research is no minor event: researchers have figured out how to reprogram adult cells into a state that is nearly indistinguishable from that of embryonic, pluripotent stem cells. This is huge news that promises to accelerate the pace of research in the field.

The problem has always been that cells exist in distinct states. A skin cell, for instance, has one set of genes essential for its specific function activated, and other sets of genes turned off; an egg cell has different patterns of gene activation and inactivation. Just taking the DNA from a skin cell and inserting it into the egg cell isn’t necessarily going to create a functional egg cell, because genes essential for egg cells may be switched off in the skin cell DNA, and we don’t know how to specifically switch them on. The process of somatic cell nuclear transfer has been hit or miss for that reason, with very high failure rates—scientists are basically trying to make the right configuration of genes switch on by giving the nucleus a good hard kick, and hoping that something in the cells will reconfigure the pattern of gene activation into something appropriate.

What the discovery by Takahashi et al. accomplishes is to reveal how to specifically switch on the right pattern of genes for a pluripotent stem cell. They have discovered the reset button for mammalian cells: a simple trigger that puts the cells in the right state to become anything else.

In 2005, a federal judge banned Pandas outright from science classrooms in Dover, Pennsylvania — but only after denying FTE [Foundation for Thought and Ethics] the right to appear before the court to defend the book.

Hmmm. Why does that sound odd?

Maybe because Jon Buell, President of FTE, did actually appear in the courtroom of Judge John E. Jones III, and there attempted to defend the book. Of course, Buell made a laughingstock of himself, of FTE, and of the sham called “intelligent design” – pretty serious work for just one day in court, I’d say. NOVA’s focus on the bad boys of the Kitzmiller v. DASD case could have been filled out to three “B”s, Bonsell, Buckingham, and Buell, if only Jones had ruled favorably on FTE’s motion to intervene.

Who is to blame for FTE’s inability to take part in the trial portion of KvD? It isn’t Judge Jones. This is a matter of public record, something that Luskin should have been aware of before spinning stuff. One can make a case for either FTE President Jon Buell or IDC advocate and FTE Academic Editor William A. Dembski having tripped up on this one, as becomes clear with just a small excursion to the transcript of the court’s consideration of FTE’s motion to intervene. At the time that FTE finally decided to file its motion to intervene, it was already late in May, 2005. Notably, this only happened about the time that the Thomas More Law Center and the Discovery Institute were apparently having some serious behind-the-scenes disagreements over the conduct of the case. FTE seemed to be far more willing to act on DI orders than the TMLC had proved to be, so having FTE obtain a co-defendant role in the case was likely a high priority for the DI. This may explain the DI’s continuing angst over the exceedingly poor showing that Buell had in court, so much so that they won’t even draw attention to it, but instead place blame – erroneously, of course – on Judge Jones.

Did FTE receive due process? It is hard to argue that they did not, given the copious public record demonstrating that they did. That seems to be why Luskin just tosses off a slur, apparently hoping that no one will take a closer look. There are several elements of interest in Buell’s testimony, including the howler that FTE is not a religious organization, the curious silence of Dembski, and Buell’s ignorance of the one issue that might have given FTE entry to the case.

It is one thing to correct Michael Behe, some structure guy with zero research experience on HIV-1 evolution. But considering the sheer number of DI “fellows” who are lawyers, and the fact I’m just a biology student with zero experience in law, I found it rather strange that I caught something the DI lawyers evidently had no problem with:

“Five states (Kansas, New Mexico, Pennsylvania, South Carolina, and Minnesota) have already adopted science standards that require learning about some of the scientific controversies relating to evolution.”

But on page 13, they declare that

“Four states (Minnesota, New Mexico, Pennsylvania, and South Carolina) have science standards that require learning about some of the scientific controversies relating to evolution.”

To summarize the recent Open Letters series, some time ago a student of HIV, Ms Smith posted a list of binding sites found in the HIV-1 protein Vpu that contradicted Dr. Behe’s assertion that HIV has evolved no new protein-protein binding sites. Central to this was the demonstration that HIV-1 Vpu had evolved into an ion channel, a viroporin. Over two months later, Dr. Behe wrote a response, which did a disservice to Ms Smith on many levels, most especially by ignoring the key argument about Vpu viroporin. I remonstrated with Dr. Behe about this in an Open Letter. Dr. Behe publishing a series of responses to this open letter, which I responded to post by post as they were published.

As you may realize, Dr. Behe has finally conceded that he was wrong, and Vpu viroporin represents a real example of protein-protein binding. I have suggested that he issue an erratum to this effect, thanking Ms Smith for bringing this example to his attention (and the HIV Vpx duplication, which he also claimed didn’t exist). This is the very stuff of science, we all at some stage support ideas that were wrong, but when we realize they are wrong, we give them up. I thank Dr. Behe for acknowledging his mistake.

Along the way we have also learned that Dr. Behe’s citations don’t actually support his statements in “edge of Evolution”, his estimation of HIV mutation rates and effective population numbers is off by orders of magnitude, and his rationale for excluding viral protein-cellular protein binding has no biological basis (and is inconsistent).

For ease of perusal, I have put the links for all the Open Letters into this one post.

The Original Open Letter, where I protest at Dr. Behe’s treatment of Ms Smith.An Open Letter Part 2, where I detail Vpu viroporin and point out that Dr. Behe’s references do not support his assertions.An Open Letter Part 3, where I chide Dr. Behe for his continuing poor treatment of Ms Smith.An Open Letter Part 4, where I go into more detail about why Dr. Behe’s attempt to exclude certain binding sites is not valid.An Open Letter Part 5, where I dig even deeper into binding sites, and show why Dr. Behe’s attempt to exclude certain binding sites is not valid in even more detail.An Open Letter Part 6, where I point out that Dr. Behe’s population and mutation rate estimates for HIV are wrong by orders of magnitude.An Open Letter Part 7, where I thank Dr. Behe for admitting he was wrong, point out that “impresessedness” is not a biologically valid standpoint, and show that yet another reason for excluding viral protein-cell protein interactions is invalid.

Steven Novella made a point on the recent episode of The Skeptic’s Guide to The Universe (best podcast ever, by the way), and on his blog Neurologica that I thought deserved underlining. Discussing the transitional fossil Tiktaalik, which lies between modern fishes and modern amphibians, Novella points out:

What is especially cool about Tiktaalik is that the researchers, Edward B. Daeschler, Neil H. Shubin and Farish A. Jenkins, predicted that they would discover something like Tiktaalik. These paleontologists made the prediction that such a transitional form must exist in order to bridge the gap between fish and amphibians. Even more, they predicted that such a species should exist in the late Devonian period, about 375 million years ago.

So they spent several years digging through the earth on Ellesmere Island in Northern Canada, because geological and paleontological evidence suggested that exposed strata there was from the late Devonian. They predicted that, according to evolutionary theory, at this time in history a creature should have existed that was morphologically transitional between fish and amphibians. They found Tiktaalik - a “fishopod,” beautifully transitional between fish and amphibians.

But wait, I thought the creationists had told us that evolution wasn’t subject to experiment…?

Michael Medved, nationally syndicated talk radio host and bestselling author, has joined the Discovery Institute in the role of senior fellow. The position cements a longstanding friendship and recognizes a commonality of values and projects across a spectrum of issues.

Skeptical? Good! There are data to listen to on this page; look for show# 232, Monday February 19, 2007, “Big Foot With Michael Medved,”
“Medved talks about recent news reports that there is a Big Foot.”

Dan Sytman, Michael’s producer and partner on the radio show, once saw Bigfoot at the edge of a summer camp in the woods. Even before meeting Dan, Michael was a passionate believer in Sasquatch.

If you listen to the whole radio segment, be advised that the “severed foot of a Sasquatch found in Spotsylvania County, VA” that was discussed at length turned out to be simply the skinned Hind Paw of a Bear the next day.

Sir Nick of the Matzke Clan actually had to endure listening to Medved trot out the usual creationist canards on his show, back in December 2004, but assures us that

…it was great fun, although during the show I felt a bit like a hobbit in the Mines of Moria scenes from the movie the Fellowship of the Ring: Look out, Medved’s first move is flagrant baiting! [octopus monster] Uh-oh, here comes the bacterial flagellum [big goblin], and on its heels the Second Law of Thermodynamics! [little goblin]. Then, the Discovery Institute list of 300 [“They have a Cave Troll.”]

Now if you had engaged with this in your response to Ms Smith, my respect for you would have risen immeasurably. To those of you not familiar with graduate and post graduate education, we actually want graduate students to disagree with us, robustly. After all, they are the ones carrying the torch of critical enquiry when we are gone. We don’t want them to accept our say so, “just because”. As scientists and educators our brief goes beyond just those PhD students we supervise, but to all engaged in critical enquiry, regardless of how we feel about their actual mode of delivery [1].

By “playing the man”[2] Dr. Behe, rather than engaging with Ms Smith’s arguments, you abrogated our responsibility as mentors and educators. Imagine the difference if you had dealt with Vpu Viroporin straight up. How about apologizing to Ms Smith now?

I do hope that you will now publish an erratum for your book, where you acknowledge Vpu viroporin. But again you engage in the “unimpressed” rhetoric. It matters not whether we are impressed or not by the outcome of the binding, the fact is that you have claimed that binding of two (or more) proteins to each other is statistically unlikely. It doesn’t matter what they do when bound (after all, as I have repeatedly pointed out, your own example is the haemoglobin S point mutation, which just glugs things up).

ArsTechnica has an interesting article on the next tactic that ID proponents will be taking: first, sow doubt about evolution in high schools, and then push for the teaching of ID in colleges. Hat tip: NoodleFood, which concludes, “the target of Intelligent Design is not just evolution, but the very metaphysics that makes science and technology possible.” Indeed, as I argue in my forthcoming Chapman Law Review article, we seem to be seeing an increasing tendency among ID proponents to embrace postmodernist theories to argue that science and creationism are just equally valid “myths” which deserve equal time under the Establishment Clause. (I will post that article as soon as I am able.)

We had a seminar from Marco Restani of St Cloud State University yesterday — he's a wildlife biologist who talked about Tasmanian Devils. Just a little tip: don't ever invite wildlife biologists or conservation ecologists to give talks. They are the most depressing people in the world, and they really make it hard to hide away from the ugly realities. This talk was no exception: the Tasmanian Devil is in big trouble, and is facing at least two major threats, each of which may be sufficient to wipe them out. And just looke at that guy! He's adorable! How can you let them go extinct?

Reflecting on your previous post, and the current one, I would like to note that both your mutation rates (10-4) and effective population size (109-1010) are too high. By a factor of around a hundred thousand.

The commonest estimates for HIV mutation rates are between 1x10-5 and 4x10-5, with 2.5x10-5 the most common. Well, what’s a half log unit between friends? More serious is your population size estimate. Here I’d like to introduce you to the concept of effective population size.

Kudos to PBS, it looks like they’ve put up the transcript and the video of “Judgment Day” a day early. Since there are various reports of PBS stations skipping or editing the show to avoid offending their viewers (or something – I guess reality offends some people, but you would think they wouldn’t watch Nova at all in that case), this is all for the good.

Last August, when I was at the Sci Foo camp, Paul Sereno brought along the skull of one of his latest discoveries…and whoa, is it ever a weird one. This is Nigersaurus taqueti, an herbivorous dinosaur with specializations for ground-level grazing. Look at this picture; in reality, it's even more striking.

Those jaws and teeth—they are so neatly squared off and flat-edged. In addition, the skull itself on the spinal column is turned habitually downward. This is a creature that kept its face pressed to the ground as it nibbled its way across the landscape.

Another feature that was apparent is that the skull is awesomely light — it's mostly empty spaces with a delicate webwork of bony struts holding it together. It's so specialized it's almost comical, and you can imagine something like this appearing on the Flintstones as a lawn mower or hedge trimmer.

It was very interesting to see the Nova broadcast recounting the Dover
“intelligent design” trial of two years ago. The furor over the Dover trial
may have died down, but by no means is creationism dead in this country.
Each time they are beaten in court, they find another way to disguise their
religious motives and try to get around the separation of church and state.
Legally, they can’t win, but they are still very powerful in the local
communities, where school boards are easily swayed by their phony arguments
and ability to mobilize lots of church-going folks to attend school board
meetings and vote for their candidates.

Both the old-fashioned “young-earth” creationists, i.e. people who
believe the earth is only 10,000 years old, and the newer ID creationists
push their cases largely by making demonstrably false claims about evolution
and the fossil record. Their lies about the fossil record are particularly
irritating to geologists and paleontologists because creationists make
these claims without any formal training in paleontology, and without any
first-hand experience with fossils, or publications in the peer-reviewed
scientific literature. They wave their PhDs on the covers of their books,
but almost none of them have any relevant training in fossils. Some of the
claims you might still find in their books and blogs:

The “Cambrian explosion” was an instantaneous creation event. Not
true—in the past 40 years, paleontologists have documented a
3.5-billion-year history of life from single-celled organisms to
multicellular soft-bodied fossils to animals with small shells and
culminating with the trilobites and other fossils that mark the early
Cambrian Period. Modern dating techniques show this transition took at least
20 million years, and probably longer—hardly an “explosion” in anyone’s
sense of the word! Yet creationists of all stripes wave this red herring and
ignore the past 40 years’ worth of research.

There are no transitional fossils. Not true—in my new book,
Evolution: What the Fossils Say and Why It Matters, I document dozens of
transitional sequences of fossils, showing the evolution not only of
individual lineages, but also of transitional forms that span the gaps
between major groups—the “macroevolution” that creationists deny.

Humans did not evolve from ape-like ancestors. Not true—the past 50
years have yielded an amazing array of hominid fossils that provide more
than enough “missing links.” Even if there were no fossils, your own genome
is 98% identical with that of a chimpanzee. Every one of your cells is
testimony to the fact that humans are a product of evolution!

As poll after poll shows, most Americans do not know much about
evolution (or science in general), and at least 40% of Americans still
believe in the creation myths of the Bible. This is in striking contrast to
nearly every other country in the industrialized world, which long ago came
to terms with evolution, and have much higher rate of science literacy than
Americans do. Our poor science literacy is a national shame, especially in
a country where science and technology are so essential and still
world-class (at the moment). If these trends continue, however, will we soon
be outsourcing many of our science and technology to other countries, as we
do our white-collar and blue-collar jobs?

Dr. Donald R. Prothero is a Lecturer in Geobiology at Cal Tech and a Professor of Geology at Occidental College. His new book, published by Columbia University Press is Evolution: What the Fossils Say and Why It Matters.

It is good to see that you agree that the Golgi targeting sequence is an example of a binding site. However, you don’t get to ignore it because “viral proteins are special”. As I showed in the post you are supposed to be replying to, this is nonsense. In your book you categorically state HIV has developed no new binding sites, the diagram on page 145 of “Edge of Evolution” has a big zero on it. Yet your own example of a binding site is the haemoglobin S mutation, a single amino acid mutation that just clumps up proteins. You don’t write in your book “HIV has evolved several binding sites, but they don’t count because they are viral-protein-host protein interactions” or “HIV has evolved several binding sites, but they don’t count because they are equivalent to the HbS mutation”, you just write zero

Which is wrong.

An again, you are inconsistent, you are perfectly happy to consider viral-protein binding to cellular protein interactions when you think there is no evidence of them evolving (the gp120-cell surface receptor binding, CXCR4 binding anyone). Still, let us accept that you will ignore any viral-protein-cell protein interaction.

Why did you ignore the viroporin section? An example of viral-protein –viral protein interaction that generates a new structure with important functional consequences. This is a direct challenge to the very heart of your argument.

Also, Matthew Chapman, great-great grandson of Charles Darwin, put out a call yesterday for, “a Presidential Debate on Science.” I am cynical enough to think that is unlikely, given that there are usually only 3 major debates, but it is worth thinking about pushing the idea – heck, maybe at least a few science-related questions will get raised in the campaign. Unfortunately, the comments section was evidently flooded by creationists, so PT people might want to chip in their 2 cents over there.

Lastly – what did you think? Quite something seeing stuff on TV that first came to the public via PT back in 2005, no? I have now heard several requests for a “cdesign proponentsists” T-shirt…here is one try, although I think it would be most compelling with a “Evolution of Creationism” or “The Missing Link” title (or maybe the front has the evolution of creationism and the back has the missing link…anyone who is inspired may use the graph, by the way).

I checked out a few of the blogs by the usual suspects this morning, and noticed that the creationists are largely silent (so far, give 'em time) on the Dover documentary from last night…with one exception. The Discovery Institute's Media Complaints Division is wound up over it. They have an eight-point "rebuttal" of the documentary that consists of many picked nits and regurgitated whines, and I thought about taking them on point by point, but then decided it wasn't worth it. For one thing, it's written by Casey Luskin, the DI's small mammal mascot, who is something of an incompetent pipsqueak, so it's hardly worth flicking him around any more. Most importantly, it misses the point of the program entirely.

If you've seen it, think back. What was the story it told? It has two parts.

First, it made the case that Intelligent Design is not science. This is the part that I liked best; scientists came on, schooled the court on the basics of evolutionary biology, and showed them what science is, by empirical example. The documentary supplemented that with lovely animations and diagrams that illustrated the points well. Then they showed that the witnesses for Intelligent Design failed to even come close to the standards of good science, and were in fact trying to rewrite the meaning of science to sneak their doctrines into the classroom.

Second, it showed that Intelligent Design is religion in disguise. The proponents of the changes in Dover, Bonsell and Buckingham, were young earth creationists with a patent religious agenda. The book, Of Pandas and People, which was written by people associated with the Discovery Institute and which was promoted by the DI, was rooted in creationism and got a face lift in response to court decisions that ruled against creationism. And the Discovery Institute itself was founded with a sectarian religious purpose (the first words in the Wedge document are "The proposition that human beings are created in the image of God is one of the bedrock principles on which Western civilization was built.")

These are the premises that were tested in the court case, and these were the ideas illustrated in the documentary. The Discovery Institute "rebuttal" doesn't even touch these issues; their objections don't address the thrust of the court decision, which was accurately portrayed. The story is very simple, and this is all we need to say: Intelligent Design is not science, and Intelligent Design is a religious idea. That's the message, and that's the decision of a major court case, and that's what the scientists have been saying for years. And now, in the desperate gasp of the creationists, they've failed to even touch these conclusions.

November 13, 2007 – The National Center for Science Education congratulates the producers of Judgment Day, a documentary about the seminal Kitzmiller v. Dover trial of 2005, for its accurate portrayal of the case that showed intelligent design to be a specific religious viewpoint. Judgment Day premiers on November 13, 2007, on PBS stations nationwide.

NCSE served as a consultant for the plaintiffs’ successful legal team in the case, and three members of its board of directors – Kevin Padian, professor of integrative biology at the University of California, Berkeley; Barbara Forrest, professor of philosophy at Southeastern Louisiana University; and Brian Alters, professor of education at McGill University – testified as expert witnesses at the trial.

Research in the NCSE archives played a crucial role in demonstrating the links between intelligent design and previous forms of creationism. “They tried to make an end-run around an earlier generation of legal rulings by switching the word ‘creation’ to ‘intelligent design’ in drafts of a creationist textbook,” commented Nick Matzke, NCSE’s scientific consultant for the Dover plaintiffs and now a doctoral student in integrative biology at the University of California, Berkeley. “We found documents in the NCSE archives which were ‘missing links’ in this evolution of creationism.”

Many viewers seem to have been surprised by the transitional fossil between creationist and cdesign proponentsists so here is an original posting by Nick Matzke on Missing link: “cdesign proponentsists”

Several of us (Pharyngula and The Atheist Experience and Greg Laden) have live-blogged the PBS documentary on the Dover trial…if you are in some other time zone or missed the show, you can find out what happened!

I will spoil the ending for you a little bit: the good guys win, and the documentary clearly shows us why.

I’m sorry you couldn’t follow Ms Smith’s argument. I found it quite easy, an elegant detective story that built up its case clue by clue. However, even if you couldn’t follow it, the viroporin story was pretty hard to miss. That Vpu evolved over the space of a decade, when viral numbers were low, into a viroporin, a multisubunit structure with a function previously absent from HIV-1, was an obvious key challenge to your assertions.

Indeed, it’s over the top enough that I never could actually get angry with the place. Not that I was planning to; I admit to dreading coming to the place, but that’s primarily because I thought it would bore and annoy me, not make me angry. In fact, I was never bored, and was genuinely annoyed only by the “paleontologist” at the start of the walk-through. The rest of the time I enjoyed it as I suspect anyone who is not some stripe of creationist could enjoy it: As camp. At some point — specifically the part where the Scopes Monkey Trial was presented as the end of decent Christian civilization as we know it — I just started chuckling my way through. By the time I got to the Dinosaur Den, with its placards full of patent misinformation about how soft tissue fossilization strongly suggested a massive, worldwide flood, I was a little loopy. It was just so ridiculous.

There's some understanding for why the silly place is popular (apparently, attendance is quite good), and a recognition that it's all one big, ridiculous joke.

Thanks to one of our commenters for pointing out this website that calculates the reading level of blogs. Just for fun I inserted UD and it came back “High School,” which means that the general discussion at this blog is at a high school level. I then inserted Pandas Thumb and it came back “Elementary School.”

Make of this what you will.

So I checked it and indeed, UncommonDescent came back as “High School” but Pandas Thumb came back as “College Post Grad”

I have just read your first response to my open letter to you. Is this what your argument is reduced to? A list of examples of Ms Smiths alleged uncivility to you. I find this rather sad

Yes, science is about civil discourse. And we, as experienced scientists are guardians and upholders of this discourse. We teach by example. If someone is discourteous to us, we reply courteously, and continue to reply courteously in the face of adversity. We keep to the topic and discuss the substantiative issues raised. We do not engage in petty sexism, we do not completely ignore someone’s core argument and discuss trivialities.

This is my central disagreement with you [1]. You avoided the issue. As educators, we lead by example. What example do you think it sets to avoid the major substantiative issue that Ms Smith raised?

Dr. Behe, regardless of how you feel about the tone of Ms Smiths discourse, you need to engage with the fact that HIV-1 M Vpu is a viroporin, a new mini-“molecular machine” that has arisen since HIV evolved from SIV. In science, there can be no greater discourtesy than ignoring a key, substantial argument. Until you engage with Vpu viroporin, your professionalism is on the line.

Yours sincerely

A male featherless biped named Ian Musgrave[2,3]

[1] The casual sexism issue is important too, but I leave that to others.
[2] As I said before I’m a Senior Lecturer in the Australian system. Even though it is roughly equivalent to a US professorial appointment, calling me a professor is misleading. Dr. Musgrave is my appropriate title.
[3] Once again Dr. Behe. I invite you to be co-respondent on “The Vpu Debate” blog, to avoid all this backing and forthing.

We are nearing the end of the year and and the submission deadline for The Open Laboratory: The Best Writing on Science Blogs 2007, edited by Bora and myself. Go here to submit quality science blog posts before the deadline ends, Dec 20th. Bora has a list of the current submissions, so if you seen any good posts not represented go ahead and submit them.

Now comes the hard part. I need 20-25 science bloggers and science blog readers to volunteer to judge the quality of the submissions. You won’t have to read hundreds of entries, just the ones in the categories that you are assigned. I’m planning on using the following categories (subject to change):

The fine folks at the Discovery Institute aren’t happy with tomorrow’s PBS documentary on the Dover Intelligent Design case, and they’re doing their best to make sure that everyone knows just how unhappy they are. They’ve been frantically tossing articles up on their Media Complaints Division Blog trying to make sure that their version of reality gets some exposure. I’m not going to bother going through all of their complaints right now. Most of their new material consists of a rehashing of discredited arguments from when the ruling came out. There’s one post that caught my eye, though, mostly because it’s such a fantastic exemplar of the level of honesty and academic discourse that makes Discovery what it is.

The NCSE reports that Nature has reviewed “Judgment day” and praised it

“Judgment Day gracefully avoids ridiculing intelligent design for the pseudo-intellectual fundamentalist fig-leaf that it is, by simply showing how the protagonists shot themselves in the foot,” Rutherford adds. Acknowledging that the “intelligent design” movement is still alive in the wake of the trial, he nevertheless concludes that “the Kitzmiller vs Dover verdict, matched this September with the outlawing of intelligent design in the UK national curriculum, marked the official neutering of this unpleasant, sneaky movement in much of the western world. Judgment Day is just the sort of thoughtful programming that celebrates how sensible people – faithful and otherwise – can use science and reason to combat fundamentalism.”

Abbie Smith has recently responded to your reply to her article on the HIV-1 protein Vpu. To refresh your memory, Ms Smith showed that the recently evolved viroporin activity of HIV-1 Vpu directly contradicts your statement that HIV has evolved no new binding sites since it entered humans (see “Edge of Evolution”, page 145 and 146). I see you intend to reply to my open letter at your Amazon blog, rather than engaging in open discussion here, or better yet, doing Ms Smith the courtesy of replying on her own blog. I hope that at least this time you will reply to the key argument Ms Smith made:

HIV-1 M Vpu is a viroporin.

SIV Vpu is not a viroporin, HIV-1 O Vpu is not a viroporin. This is a new activity that evolved in HIV after the split from SIV over a 10 year timeframe and is part of the reason that the HIV-1 M clade is the most common type of HIV in the world.

Also, I have just heard that Kenneth Miller will be interviewed on NBC’s Today Show on Monday morning, opposed by Steve Fuller. Note to Today Show staff: make sure you give Fuller decaf.Update: this segment of the Today Show has been canceled at the last minute. So, never mind.

For the last few years (beginning, I believe, in 2004) a lot of noise has been filling a number of websites regarding the “conversion” of British author Antony Flew from atheism to deism. Recently a new book, ostensibly authored by Flew, was published by HarperCollins, wherein Flew’s newly adopted deistic worldview is defended. Two Christian propagandists, Roy Varghese and Bob Hostetler, and, indirectly, Jewish religious propagandist Gerald Schroeder seem to have played a substantial role in producing that book. (See, for example, here.)

Some advocates of theism try to present Flew’s “conversion” as a supposedly important event somehow proving their beliefs. Is it indeed an important event deserving numerous posts and articles? Let us see.

ID supporters seem to like Antony Flew, the one-time atheist philosopher who has apparently seen the light and become a deist. They have awarded him the Phillip Johnson Award for Liberty and Truth, they have lauded his latest book, and Bill Dembski exclaims "God bless Antony Flew!" But at the risk of raining on the parade, there’s something that Bill needs to realize - the fearless Flew seems to have a very ambivalent attitude (to put it mildly) to eugenics.

Those crazy folks over at the Alliance for Science are putting up the notice for their 2nd Annual Evolution Essay contest!!! The first contest, while thrown together at the very last minute, turned out to be a success. Five high school students received cash prizes and a slew of autographed science books, plus a year’s subscription to Seed Magazine. The first place winner’s science teacher also received a cash prize to spend on classroom supplies, and additional teaching materials.

This year, they’re getting a jump on things early. The contest doesn’t happen until February, but start thinking about your essay now. Tell your teachers so they can get their classrooms involved. This year’s topics are rather timely: Climate, Agriculture, and Evolution.

The Alliance is also looking for a little help on the judging side of things, so please contact them if you’re interested. And as always, if you wish to donate a copy of a book or contribute financially to the prizes, all donations are tax-deductible.

There has been another tragic shooting at a school, this time at Jokela secondary school in Tuusula, Finland. It was a single gunman on a rampage, and at least seven people have been killed.

We're going to hear much more about this because the murderer claims to have carried out this act in the name of natural selection. Some of the murderer's files are available online (so far; that link may not function for long), and they portray a sick man with a distorted view of evolution that he used to justify his actions.

Editors in chief Dr. Niles Eldredge, Ph.D., Curator
of the Division of Paleontology at the American Museum of Natural History in New York, New York and Gregory Eldredge, M.A. at the John F. Kennedy High School in the Bronx, New York have announced a new journal titled Evolution: Education and Outreach Launching at the conference of the National Association of Biology Teachers, November 28-December 2, Atlanta.

*** Evolution: Education and Outreach will be free online during 2008! ***

Darwin’s Theory of Evolution revolutionized scientific thinking. Since the publication of The Origin of Species 147 years ago, this theory has been extensively and rigorously tested. Overwhelming scientific evidence from many disciplines exists to support this theory. From the vast body of scientific evidence that has accumulated, we have come to an understanding of all areas of the biological world - from our cells and DNA to our lakes and forests. Evolutionary principles are the foundation of all modern biology and have led to major advances in fields as diverse as molecular biology, developmental biology, genetics, behavior, and paleontology. As such, evolutionary theory is a fundamental and necessary component of modern science education.

Evolution: Education and Outreach will promote accurate understanding and comprehensive teaching of evolutionary theory for a wide audience. Targeting K-16 students, teachers and scientists alike, the journal will publish articles to aid members of these communities in the teaching of evolutionary theory.

The funny thing is how both Behe and the DI claim that I don’t address the substance of Behe’s book, all while ignoring the substance of my review, which addressed the substance of Behe’s book. All they can do is splutter that I am a biased reviewer who until recently worked at NCSE and therefore I must be wrong. (This, by the way, is how you know when you’ve got creationists where you want them.) I’ll make a list of my points and the non-replies below. It’s pretty shocking what they missed, considering my review was only 800 words or so, one of the shortest ones out there.

The National Association of Science Teachers produces a biweekly podcast on “science teaching, science news, and anything with ‘science’ in it.” . The current podcast, available here, is an interview with Sean B. Carroll, author of The Making of the Fittest and Endless Forms Most Beautiful, about evolution, his new project, and science literacy. Highly recommended.

Therein lies the rub. What other explanations could there possibly be that are nonreligious? (Besides extraterrestrials.) Intelligent design advocates such as Voss might not openly call for classroom lectures on “looks like divine intervention!” But the implicit conclusion is nigh unavoidable. Intelligent design (note the expression!) in public schools functionally guarantees teaching/discussing religious ideas as “truth.”

We can explore that. If my inference is correct, what “unavoidable conclusion that is a religious belief” might intelligent design advocates have in mind? Dare we ask how many want this who are not Christian? (In fairness, perhaps Voss is no more a theist than Dawkins et al.) Could they live with students embracing deism? Islam? Buddhism? Classical philosophy? Anything besides Christianity? Or is the intent to promote some vague generic theism? And why would a committed member of any religious tradition hope for such a thing? Be careful what you ask for.

Be honest and tell us openly. Although difficulties with evolutionary theory probably should be acknowledged, exactly what “other explanations” will be presented and discussed – and accepted? I honestly cannot find how Voss would answer.

The estimates for chloroquine and artemisinin are speculative. In the former case, this assumes two events in 10 years of use with exposure of 10% of the world’s falciparum malaria (Burgess &Young 1959; Martin&Arnold1968; Looareesuwan et al. 1996; Su et al. 1997

Luskin is correct, the number is not a “mere guess”, it’s a speculative estimate. Glad we got that right. Why Luskin failed to mention this is beyond me since he does seem to quote the paper in question. Perhaps if Luskin had spent more time on reading the papers and less on emphasizing the academic achievements of White, he might have found the error in Behe’s claim himself.

What Behe meant when he said that

the 1020 statistic is an empirically derived fact

is less clear. Surely since ID proponents are so critical of evolutionary scientists when it comes to confusing fact and fiction, Behe may wants to revise his statement.

The best I can say after reading and then rereading Mark Oppenheimer’s article, “The Turning of an Atheist,” in today’s New York Times Magazine
( http://www.nytimes.com/2007/11/04/m[…]4Flew-t.html )
is that Antony Flew is not the man he once was and has been out of touch for some time. Readers of PT will recall his recent conversion to deism, which he based on the “teaching” of the old-earth creationist, Gerald Schroeder. Professor Flew recanted his acceptance of Schroeder but maintained his belief in a god - a deistic god, however, not a personal god, and certainly not the God of Christianity.

Now, according to Mr. Oppenheimer, Professor Flew acquiesced when Roy Abraham Varghese, an eastern-rite Catholic, ghost-wrote a book under Professor Flew’s name. Much of the manuscript was book-doctored by an evangelical pastor, Bob Hostetler. Though Professor Flew allegedly vetted the book, it is hard to know how much he truly approved of; he freely told Mr. Oppenheimer that he suffers from a form of aphasia and did not recognize the names of several philosophers mentioned in the book. Similarly, he could not recall conversations that took place in the last year or two and could not define certain words used frequently in the book. Professor Flew is 84 years old.

Mr. Oppenheimer makes a valiant attempt not to conclude that Professor Flew is being exploited, at least not deliberately. It is a noble effort, but it is hard to agree with him.

In the Orlando Sentinel, Mike Thomas reports on some good news in the state of Florida

We are moving toward intelligently designed science curriculum in public schools.

And by that I mean we are leaving intelligent design out of classrooms.

By golly, Florida is evolving.

After receiving failing marks in teaching evolution, Florida is revising its curriculum.

The standards are based in part on those used in countries that excel in science, such as Singapore and Finland. Massachusetts is another role model. The National Science Education Standards and National Assessment of Educational Progress also are cited.

“These new benchmarks are based on research,” says Mary Jane Tappen, executive director of math and science for the Department of Education. “What research says should be in the standards.”

Ok people want more science, let’s give them what they are asking for. Most of us are familiar with the claims by creationists that most or all of the mutations are found to be detrimental. And before anyone calls this a strawman, remember that it was Ray I believe who insisted on a 100% detrimental mutation rate. In addition, ID proponents seem to take seriously Sanford’s concept of ‘genetic entropy’ which based on what I have read about his argument is a rejuvenated 2nd law of thermodynamics argument. Of course, most familiar with science would understand that most mutations are neutral and that some are detrimental and few are beneficial. However, recent research has shown that the beneficial mutation rates are much higher than originally expected.

The central role of beneficial mutations for adaptive processes in natural populations is well established. Thus, there has been a long-standing interest to study the nature of beneficial mutations. Their low frequency, however, has made this class of mutations almost inaccessible for systematic studies. In the absence of experimental data, the distribution of the fitness effects of beneficial mutations was assumed to resemble that of deleterious mutations. For an experimental proof of this assumption, we used a novel
marker system to trace adaptive events in an evolving Escherichia coli culture and to determine the selective advantage of those beneficial mutations. Ten parallel cultures were propagated for about 1,000 generations by serial transfer, and 66 adaptive events were identified. From this data set, we estimate the rate of beneficial mutations to be 4 x 10-9 per cell and generation. Consistent with an exponential distribution of the fitness effects, we observed a large fraction of advantageous mutations with a small effect and only few with large effect. The mean selection coefficient of advantageous mutations in our experiment was 0.02.

Not to be outdone, researchers in 2007 reported on a rate which was another 1000 times faster

Creationists and supporters of Intelligent Design Theory (“IDers”) are fond of erecting a strawman in place of evolutionary theory, one that they can then dismantle and point to as “proof” that their “theories” are superior. Perhaps the most egregious such strawman is encapsulated in the phrase “RM & NS”. Short for “random mutation and natural selection”, RM & NS is held up by creationists and IDers as the core of evolutionary biology, and are then attacked as insufficient to explain the diversity of life and (in the case of some IDers) its origin and evolution as well.

Evolutionary biologists know that this is a classical “strawman” argument, because we know that evolution is not simply reducible to “random mutation and natural selection” alone. Indeed, Darwin himself proposed that natural selection was the best explanation for the origin of adaptations, and that natural selection itself was an outcome that necessarily arises from three prerequisites:

• variation (between individuals in populations),
• inheritance (of traits from parents to offspring), and
• fecundity (reproduction resulting in more offspring than necessary for replacement).

Given these prerequisites, some individuals survive and reproduce more often than others, and hence their characteristics become more common in their populations over time.

Allen lists 43 sources of variation (as a minimum) and “at least three different processes that result from them: natural selection, sexual selection, and random genetic drift.”

On EvolutionNews, Robert Crowther creates a strawman and knocks it down by confusing the term “Darwin Skeptic” with “Intelligent Design proponent”. Remember that the claim is not that all Darwin skeptics are religious fundamentalists but rather that ID is irreparably tied to religious concepts and motivations and lacking in scientific content.

Remember that Berlinski is on the record as “I have never expressed support for theories (sic) of Intelligent Design…”. or the following excerpt in which he distances himself from Intelligent Design?

Berlinski Wrote:

“If I thought that intelligent design, or any artful contrivance like it, explained anything in any depth, I would leap to the cannon’s mouth and say so. I do not and I did not.” For the record: I do not believe that theories of intelligent design explain those features of living systems that Darwin’s theory of evolution fails to explain. And vice-versa.

Last summer, I had it out with Uncommon Descent’s Salvador Cordova on the topic of Genetic Algorithms (GA’s). During this series of posts, I explained that Dawkin’s use of a Targeted genetic algorithm - one that looks for the specific phrase “Methinks it is like a weasel” in simulations of selection and reproduction - was intended as a tutorial example only, and does not (as Dawkins himself pointed out way back in 1986) provide a rigorous simulation of evolution. Since then, creationists of all stripes have tried time and again to smear all Genetic Algorithms with the “They Need a Specified Target - just like Dawkins’ Weasel” argument.

During the series of posts, which began here, and ended here (the latter having links to the summer’s salvos from both sides), Cordova said I was just sneaking in the answer to difficult math questions (involving Steiner Trees, an NP-hard math problem) instead of having the genetic algorithm “evolve” them properly. Cordova presented an algorithm he claimed could do math problems without specifying an answer, just like mine, but I proved that his algorithm did indeed inevitably converge to an exact, specified result, quite unlike my GA for Steiner.

Even with a week’s time, and the libraries and websites of the whole world available to him, Cordova failed to derive as good an answer to the given challenge as my evolution-based GA did in just a couple of hours.

About this time, Cordova stopped railing about Dawkins, Weasels, Selection, and Targets, and started saying that computers are just plain faster than humans at solving math problems.

While Cordova’s attack on GA’s in defense of ID was feeble at best, at least he was trying to keep up with parts of the discussion.

Rather than focusing on how new information might emerge from evolutionary processes, Patrick steps into the Wayback machine, demanding that GA’s produce not just a specified phrase a la “Weasel,” but instead a complete (and completely insipid) anti-evolutionary “poem.”

I kid you not. I wonder if Dembski even knows what his silly monkeys are doing on his blog. I guess ID theorists are never critical to each other, for the same reason you rarely hear harsh words exchanged publicly between members of the same church.

The date is nearing when the PBS/NOVA program “Judgment Day: Intelligent Design on trial” will air and not surprisingly the Discovery Institute is not pleased. On EvolutionNews, Robert Crowther, director of media and public relations, complains that:

Robert Crowther Wrote:

The trailer for the program shows that PBS has turned to the usual suspects to advance their agenda.

Yes, such people as “Father of Intelligent Design” Philip Johnson or Steve Fuller did participate and what is even more ironic is that many more Discovery Institute people were asked to participate but they declined.